Starting phenix.real_space_refine on Thu Feb 15 13:52:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0j_31399/02_2024/7f0j_31399.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0j_31399/02_2024/7f0j_31399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0j_31399/02_2024/7f0j_31399.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0j_31399/02_2024/7f0j_31399.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0j_31399/02_2024/7f0j_31399.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0j_31399/02_2024/7f0j_31399.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 64 5.16 5 C 8036 2.51 5 N 2112 2.21 5 O 2208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 131": "OD1" <-> "OD2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 131": "OD1" <-> "OD2" Residue "C TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 131": "OD1" <-> "OD2" Residue "F TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 131": "OD1" <-> "OD2" Residue "H TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12424 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3105 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 14, 'TRANS': 371} Chain breaks: 2 Chain: "C" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3105 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 14, 'TRANS': 371} Chain breaks: 2 Chain: "F" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3105 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 14, 'TRANS': 371} Chain breaks: 2 Chain: "H" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3105 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 14, 'TRANS': 371} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 788 SG CYS B 132 60.801 38.204 86.720 1.00 41.28 S ATOM 794 SG CYS B 133 61.054 41.812 88.010 1.00 40.69 S ATOM 9941 SG CYS H 111 58.163 39.541 89.064 1.00 42.02 S ATOM 626 SG CYS B 111 64.873 58.163 89.064 1.00 42.18 S ATOM 3893 SG CYS C 132 66.210 60.801 86.720 1.00 41.29 S ATOM 3899 SG CYS C 133 62.602 61.054 88.010 1.00 40.67 S ATOM 3731 SG CYS C 111 46.251 64.873 89.064 1.00 42.26 S ATOM 6998 SG CYS F 132 43.613 66.210 86.720 1.00 41.20 S ATOM 7004 SG CYS F 133 43.360 62.602 88.010 1.00 40.61 S ATOM 6836 SG CYS F 111 39.541 46.251 89.064 1.00 42.18 S ATOM 10103 SG CYS H 132 38.204 43.613 86.720 1.00 41.16 S ATOM 10109 SG CYS H 133 41.812 43.360 88.010 1.00 40.55 S Time building chain proxies: 6.69, per 1000 atoms: 0.54 Number of scatterers: 12424 At special positions: 0 Unit cell: (105.825, 105.825, 134.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 64 16.00 O 2208 8.00 N 2112 7.00 C 8036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.19 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" ND1 HIS B 105 " pdb="ZN ZN B 701 " - pdb=" SG CYS H 111 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 132 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 133 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" ND1 HIS C 105 " pdb="ZN ZN C 701 " - pdb=" SG CYS B 111 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 132 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 133 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 105 " pdb="ZN ZN F 701 " - pdb=" SG CYS C 111 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 132 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 133 " pdb=" ZN H 701 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 105 " pdb="ZN ZN H 701 " - pdb=" SG CYS F 111 " pdb="ZN ZN H 701 " - pdb=" SG CYS H 132 " pdb="ZN ZN H 701 " - pdb=" SG CYS H 133 " Number of angles added : 12 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 4 sheets defined 75.6% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 69 through 75 removed outlier: 4.081A pdb=" N ASP B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 101 removed outlier: 3.612A pdb=" N PHE B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.617A pdb=" N ILE B 128 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 129' Processing helix chain 'B' and resid 133 through 155 removed outlier: 3.623A pdb=" N ARG B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 166 through 166 No H-bonds generated for 'chain 'B' and resid 166 through 166' Processing helix chain 'B' and resid 167 through 175 removed outlier: 3.980A pdb=" N VAL B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 226 through 251 removed outlier: 4.177A pdb=" N PHE B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 280 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.012A pdb=" N THR B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.501A pdb=" N PHE B 303 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.702A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.024A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.697A pdb=" N LEU B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 435 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 69 through 75 removed outlier: 4.081A pdb=" N ASP C 73 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 101 removed outlier: 3.612A pdb=" N PHE C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.617A pdb=" N ILE C 128 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 129 " --> pdb=" O PRO C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 129' Processing helix chain 'C' and resid 133 through 155 removed outlier: 3.623A pdb=" N ARG C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 166 through 166 No H-bonds generated for 'chain 'C' and resid 166 through 166' Processing helix chain 'C' and resid 167 through 175 removed outlier: 3.980A pdb=" N VAL C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 205 Processing helix chain 'C' and resid 226 through 251 removed outlier: 4.177A pdb=" N PHE C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 280 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 281 through 283 No H-bonds generated for 'chain 'C' and resid 281 through 283' Processing helix chain 'C' and resid 287 through 296 removed outlier: 4.012A pdb=" N THR C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 removed outlier: 3.501A pdb=" N PHE C 303 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.702A pdb=" N ARG C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 356 through 369 removed outlier: 4.024A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 removed outlier: 3.697A pdb=" N LEU C 392 " --> pdb=" O SER C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 435 Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 69 through 75 removed outlier: 4.080A pdb=" N ASP F 73 " --> pdb=" O SER F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 101 removed outlier: 3.612A pdb=" N PHE F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 122 Processing helix chain 'F' and resid 125 through 129 removed outlier: 3.617A pdb=" N ILE F 128 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE F 129 " --> pdb=" O PRO F 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 125 through 129' Processing helix chain 'F' and resid 133 through 155 removed outlier: 3.623A pdb=" N ARG F 147 " --> pdb=" O GLU F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 158 No H-bonds generated for 'chain 'F' and resid 156 through 158' Processing helix chain 'F' and resid 166 through 166 No H-bonds generated for 'chain 'F' and resid 166 through 166' Processing helix chain 'F' and resid 167 through 175 removed outlier: 3.980A pdb=" N VAL F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 205 Processing helix chain 'F' and resid 226 through 251 removed outlier: 4.177A pdb=" N PHE F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 260 Processing helix chain 'F' and resid 260 through 280 Proline residue: F 272 - end of helix Processing helix chain 'F' and resid 281 through 283 No H-bonds generated for 'chain 'F' and resid 281 through 283' Processing helix chain 'F' and resid 287 through 296 removed outlier: 4.012A pdb=" N THR F 291 " --> pdb=" O GLY F 287 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 305 removed outlier: 3.501A pdb=" N PHE F 303 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 320 removed outlier: 3.702A pdb=" N ARG F 311 " --> pdb=" O SER F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 347 Processing helix chain 'F' and resid 356 through 369 removed outlier: 4.025A pdb=" N TRP F 362 " --> pdb=" O PRO F 358 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR F 363 " --> pdb=" O ALA F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 400 removed outlier: 3.697A pdb=" N LEU F 392 " --> pdb=" O SER F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 435 Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 69 through 75 removed outlier: 4.081A pdb=" N ASP H 73 " --> pdb=" O SER H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 101 removed outlier: 3.612A pdb=" N PHE H 92 " --> pdb=" O ASP H 88 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS H 94 " --> pdb=" O ASP H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 122 Processing helix chain 'H' and resid 125 through 129 removed outlier: 3.617A pdb=" N ILE H 128 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE H 129 " --> pdb=" O PRO H 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 125 through 129' Processing helix chain 'H' and resid 133 through 155 removed outlier: 3.623A pdb=" N ARG H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 166 through 166 No H-bonds generated for 'chain 'H' and resid 166 through 166' Processing helix chain 'H' and resid 167 through 175 removed outlier: 3.980A pdb=" N VAL H 171 " --> pdb=" O ALA H 167 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 205 Processing helix chain 'H' and resid 226 through 251 removed outlier: 4.177A pdb=" N PHE H 230 " --> pdb=" O ALA H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 260 Processing helix chain 'H' and resid 260 through 280 Proline residue: H 272 - end of helix Processing helix chain 'H' and resid 281 through 283 No H-bonds generated for 'chain 'H' and resid 281 through 283' Processing helix chain 'H' and resid 287 through 296 removed outlier: 4.012A pdb=" N THR H 291 " --> pdb=" O GLY H 287 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG H 296 " --> pdb=" O LEU H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 305 removed outlier: 3.501A pdb=" N PHE H 303 " --> pdb=" O ILE H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 320 removed outlier: 3.702A pdb=" N ARG H 311 " --> pdb=" O SER H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 347 Processing helix chain 'H' and resid 356 through 369 removed outlier: 4.025A pdb=" N TRP H 362 " --> pdb=" O PRO H 358 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR H 363 " --> pdb=" O ALA H 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 400 removed outlier: 3.697A pdb=" N LEU H 392 " --> pdb=" O SER H 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 435 Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 44 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 44 Processing sheet with id=AA3, first strand: chain 'F' and resid 42 through 44 Processing sheet with id=AA4, first strand: chain 'H' and resid 42 through 44 792 hydrogen bonds defined for protein. 2316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3952 1.34 - 1.46: 2801 1.46 - 1.58: 5871 1.58 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 12720 Sorted by residual: bond pdb=" C TYR C 106 " pdb=" O TYR C 106 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.69e-01 bond pdb=" C TYR B 106 " pdb=" O TYR B 106 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.69e-01 bond pdb=" C TYR H 106 " pdb=" O TYR H 106 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.69e-01 bond pdb=" C TYR F 106 " pdb=" O TYR F 106 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.69e-01 bond pdb=" CB PRO B 401 " pdb=" CG PRO B 401 " ideal model delta sigma weight residual 1.492 1.533 -0.041 5.00e-02 4.00e+02 6.80e-01 ... (remaining 12715 not shown) Histogram of bond angle deviations from ideal: 100.61 - 107.30: 340 107.30 - 113.99: 7038 113.99 - 120.68: 5749 120.68 - 127.37: 4005 127.37 - 134.05: 100 Bond angle restraints: 17232 Sorted by residual: angle pdb=" C ILE B 270 " pdb=" N LEU B 271 " pdb=" CA LEU B 271 " ideal model delta sigma weight residual 120.09 123.61 -3.52 1.25e+00 6.40e-01 7.95e+00 angle pdb=" C ILE C 270 " pdb=" N LEU C 271 " pdb=" CA LEU C 271 " ideal model delta sigma weight residual 120.09 123.61 -3.52 1.25e+00 6.40e-01 7.95e+00 angle pdb=" C ILE H 270 " pdb=" N LEU H 271 " pdb=" CA LEU H 271 " ideal model delta sigma weight residual 120.09 123.61 -3.52 1.25e+00 6.40e-01 7.95e+00 angle pdb=" C ILE F 270 " pdb=" N LEU F 271 " pdb=" CA LEU F 271 " ideal model delta sigma weight residual 120.09 123.61 -3.52 1.25e+00 6.40e-01 7.95e+00 angle pdb=" N ASN C 46 " pdb=" CA ASN C 46 " pdb=" C ASN C 46 " ideal model delta sigma weight residual 110.23 113.34 -3.11 1.45e+00 4.76e-01 4.61e+00 ... (remaining 17227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 6476 14.14 - 28.27: 716 28.27 - 42.41: 272 42.41 - 56.55: 36 56.55 - 70.68: 4 Dihedral angle restraints: 7504 sinusoidal: 2964 harmonic: 4540 Sorted by residual: dihedral pdb=" CA ASN B 46 " pdb=" C ASN B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASN C 46 " pdb=" C ASN C 46 " pdb=" N VAL C 47 " pdb=" CA VAL C 47 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASN H 46 " pdb=" C ASN H 46 " pdb=" N VAL H 47 " pdb=" CA VAL H 47 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 7501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1109 0.026 - 0.052: 452 0.052 - 0.077: 237 0.077 - 0.103: 94 0.103 - 0.128: 36 Chirality restraints: 1928 Sorted by residual: chirality pdb=" CA GLN F 417 " pdb=" N GLN F 417 " pdb=" C GLN F 417 " pdb=" CB GLN F 417 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA GLN C 417 " pdb=" N GLN C 417 " pdb=" C GLN C 417 " pdb=" CB GLN C 417 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA GLN H 417 " pdb=" N GLN H 417 " pdb=" C GLN H 417 " pdb=" CB GLN H 417 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1925 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 402 " -0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO F 403 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO F 403 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 403 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 402 " 0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO H 403 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO H 403 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 403 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 402 " -0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO C 403 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 403 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 403 " -0.042 5.00e-02 4.00e+02 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3376 2.81 - 3.33: 12628 3.33 - 3.85: 20757 3.85 - 4.38: 23097 4.38 - 4.90: 39616 Nonbonded interactions: 99474 Sorted by model distance: nonbonded pdb=" O CYS C 231 " pdb=" OG1 THR C 234 " model vdw 2.281 2.440 nonbonded pdb=" O CYS F 231 " pdb=" OG1 THR F 234 " model vdw 2.281 2.440 nonbonded pdb=" O CYS B 231 " pdb=" OG1 THR B 234 " model vdw 2.281 2.440 nonbonded pdb=" O CYS H 231 " pdb=" OG1 THR H 234 " model vdw 2.281 2.440 nonbonded pdb=" OD1 ASP F 86 " pdb=" NH1 ARG H 100 " model vdw 2.318 2.520 ... (remaining 99469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.470 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 37.210 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12720 Z= 0.155 Angle : 0.538 6.566 17232 Z= 0.292 Chirality : 0.039 0.128 1928 Planarity : 0.006 0.076 2180 Dihedral : 13.592 70.682 4576 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1520 helix: 1.50 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -2.12 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 362 HIS 0.002 0.000 HIS H 306 PHE 0.010 0.001 PHE C 338 TYR 0.015 0.001 TYR F 413 ARG 0.002 0.000 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.443 Fit side-chains REVERT: B 109 HIS cc_start: 0.7478 (p-80) cc_final: 0.6199 (m170) REVERT: B 233 ASP cc_start: 0.7941 (t0) cc_final: 0.7531 (t0) REVERT: B 262 MET cc_start: 0.6732 (mmm) cc_final: 0.6250 (mmm) REVERT: C 233 ASP cc_start: 0.7936 (t0) cc_final: 0.7527 (t0) REVERT: C 262 MET cc_start: 0.6796 (mmm) cc_final: 0.6269 (mmm) REVERT: F 233 ASP cc_start: 0.7939 (t0) cc_final: 0.7529 (t0) REVERT: F 262 MET cc_start: 0.6796 (mmm) cc_final: 0.6271 (mmm) REVERT: H 233 ASP cc_start: 0.7943 (t0) cc_final: 0.7531 (t0) REVERT: H 262 MET cc_start: 0.6800 (mmm) cc_final: 0.6268 (mmm) outliers start: 0 outliers final: 4 residues processed: 280 average time/residue: 1.0589 time to fit residues: 326.0815 Evaluate side-chains 190 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 186 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain H residue 112 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 chunk 138 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 416 ASN C 46 ASN C 416 ASN F 46 ASN F 416 ASN H 46 ASN H 416 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12720 Z= 0.305 Angle : 0.596 7.824 17232 Z= 0.322 Chirality : 0.043 0.126 1928 Planarity : 0.006 0.065 2180 Dihedral : 4.530 33.493 1744 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.31 % Allowed : 12.58 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.22), residues: 1520 helix: 1.47 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.30 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 362 HIS 0.004 0.001 HIS C 414 PHE 0.024 0.002 PHE H 175 TYR 0.018 0.002 TYR H 188 ARG 0.006 0.000 ARG C 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 196 time to evaluate : 1.433 Fit side-chains REVERT: B 183 MET cc_start: 0.4660 (OUTLIER) cc_final: 0.4432 (ttp) REVERT: B 233 ASP cc_start: 0.7957 (t0) cc_final: 0.7528 (t0) REVERT: C 109 HIS cc_start: 0.7687 (p-80) cc_final: 0.6216 (m170) REVERT: C 183 MET cc_start: 0.4660 (OUTLIER) cc_final: 0.4433 (ttp) REVERT: C 233 ASP cc_start: 0.7948 (t0) cc_final: 0.7522 (t0) REVERT: F 183 MET cc_start: 0.4651 (OUTLIER) cc_final: 0.4425 (ttp) REVERT: F 233 ASP cc_start: 0.7953 (t0) cc_final: 0.7521 (t0) REVERT: H 183 MET cc_start: 0.4657 (OUTLIER) cc_final: 0.4430 (ttp) REVERT: H 233 ASP cc_start: 0.7957 (t0) cc_final: 0.7527 (t0) outliers start: 44 outliers final: 12 residues processed: 220 average time/residue: 1.0865 time to fit residues: 262.1646 Evaluate side-chains 188 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 121 PHE Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 138 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 56 GLN C 46 ASN C 56 GLN F 46 ASN F 56 GLN H 46 ASN H 56 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12720 Z= 0.295 Angle : 0.574 7.559 17232 Z= 0.312 Chirality : 0.042 0.123 1928 Planarity : 0.006 0.059 2180 Dihedral : 4.195 16.908 1736 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.31 % Allowed : 15.66 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1520 helix: 1.45 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.34 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 362 HIS 0.004 0.001 HIS F 306 PHE 0.021 0.002 PHE B 386 TYR 0.019 0.002 TYR B 188 ARG 0.005 0.000 ARG C 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 188 time to evaluate : 1.577 Fit side-chains REVERT: B 233 ASP cc_start: 0.7946 (t0) cc_final: 0.7486 (t0) REVERT: C 109 HIS cc_start: 0.7694 (p-80) cc_final: 0.6186 (m170) REVERT: C 233 ASP cc_start: 0.7936 (t0) cc_final: 0.7479 (t0) REVERT: F 233 ASP cc_start: 0.7941 (t0) cc_final: 0.7480 (t0) REVERT: H 233 ASP cc_start: 0.7949 (t0) cc_final: 0.7487 (t0) outliers start: 44 outliers final: 12 residues processed: 212 average time/residue: 1.1070 time to fit residues: 258.1844 Evaluate side-chains 173 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 146 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN C 56 GLN C 416 ASN F 46 ASN F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN H 56 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12720 Z= 0.203 Angle : 0.524 7.879 17232 Z= 0.282 Chirality : 0.040 0.120 1928 Planarity : 0.005 0.055 2180 Dihedral : 4.019 16.014 1736 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.92 % Allowed : 16.72 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1520 helix: 1.64 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.34 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 362 HIS 0.003 0.001 HIS H 306 PHE 0.019 0.002 PHE C 121 TYR 0.016 0.001 TYR H 188 ARG 0.002 0.000 ARG H 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 188 time to evaluate : 1.596 Fit side-chains REVERT: B 109 HIS cc_start: 0.7645 (p-80) cc_final: 0.6061 (m170) REVERT: B 131 ASP cc_start: 0.6113 (OUTLIER) cc_final: 0.5846 (t70) REVERT: B 225 TYR cc_start: 0.5029 (OUTLIER) cc_final: 0.4735 (m-10) REVERT: B 233 ASP cc_start: 0.8044 (t0) cc_final: 0.7590 (t0) REVERT: B 346 GLU cc_start: 0.8863 (mm-30) cc_final: 0.7785 (tp30) REVERT: C 131 ASP cc_start: 0.6111 (OUTLIER) cc_final: 0.5842 (t70) REVERT: C 225 TYR cc_start: 0.5024 (OUTLIER) cc_final: 0.4729 (m-10) REVERT: C 233 ASP cc_start: 0.8037 (t0) cc_final: 0.7585 (t0) REVERT: C 346 GLU cc_start: 0.8868 (mm-30) cc_final: 0.7783 (tp30) REVERT: F 131 ASP cc_start: 0.6116 (OUTLIER) cc_final: 0.5850 (t70) REVERT: F 225 TYR cc_start: 0.5023 (OUTLIER) cc_final: 0.4731 (m-10) REVERT: F 233 ASP cc_start: 0.8041 (t0) cc_final: 0.7583 (t0) REVERT: F 346 GLU cc_start: 0.8856 (mm-30) cc_final: 0.7770 (tp30) REVERT: H 131 ASP cc_start: 0.6109 (OUTLIER) cc_final: 0.5838 (t70) REVERT: H 225 TYR cc_start: 0.5023 (OUTLIER) cc_final: 0.4727 (m-10) REVERT: H 233 ASP cc_start: 0.8045 (t0) cc_final: 0.7590 (t0) REVERT: H 346 GLU cc_start: 0.8853 (mm-30) cc_final: 0.7775 (tp30) outliers start: 52 outliers final: 8 residues processed: 221 average time/residue: 1.1288 time to fit residues: 272.8280 Evaluate side-chains 176 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 160 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 225 TYR Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 121 PHE Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 225 TYR Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.0170 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 56 GLN C 46 ASN C 56 GLN F 56 GLN H 56 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 12720 Z= 0.450 Angle : 0.634 7.513 17232 Z= 0.343 Chirality : 0.046 0.150 1928 Planarity : 0.006 0.059 2180 Dihedral : 4.486 20.287 1736 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 4.22 % Allowed : 18.37 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1520 helix: 1.34 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : -2.41 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP F 362 HIS 0.005 0.001 HIS C 306 PHE 0.034 0.003 PHE H 386 TYR 0.024 0.002 TYR B 188 ARG 0.004 0.001 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 167 time to evaluate : 1.451 Fit side-chains REVERT: B 147 ARG cc_start: 0.5278 (tmm-80) cc_final: 0.4800 (ttp-110) REVERT: B 225 TYR cc_start: 0.5931 (OUTLIER) cc_final: 0.5596 (m-10) REVERT: B 233 ASP cc_start: 0.8166 (t0) cc_final: 0.7674 (t0) REVERT: C 147 ARG cc_start: 0.5279 (tmm-80) cc_final: 0.4797 (ttp-110) REVERT: C 225 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.5592 (m-10) REVERT: C 233 ASP cc_start: 0.8160 (t0) cc_final: 0.7670 (t0) REVERT: F 147 ARG cc_start: 0.5277 (tmm-80) cc_final: 0.4799 (ttp-110) REVERT: F 225 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.5591 (m-10) REVERT: F 233 ASP cc_start: 0.8166 (t0) cc_final: 0.7673 (t0) REVERT: H 147 ARG cc_start: 0.5281 (tmm-80) cc_final: 0.4796 (ttp-110) REVERT: H 225 TYR cc_start: 0.5926 (OUTLIER) cc_final: 0.5592 (m-10) REVERT: H 233 ASP cc_start: 0.8167 (t0) cc_final: 0.7673 (t0) outliers start: 56 outliers final: 20 residues processed: 199 average time/residue: 1.1561 time to fit residues: 251.7400 Evaluate side-chains 180 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 225 TYR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 225 TYR Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN C 56 GLN F 56 GLN H 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12720 Z= 0.241 Angle : 0.543 8.548 17232 Z= 0.291 Chirality : 0.041 0.146 1928 Planarity : 0.005 0.053 2180 Dihedral : 4.207 17.483 1736 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.71 % Allowed : 19.58 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1520 helix: 1.59 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.36 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 362 HIS 0.003 0.001 HIS H 306 PHE 0.017 0.002 PHE B 121 TYR 0.016 0.002 TYR B 188 ARG 0.002 0.000 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 189 time to evaluate : 1.455 Fit side-chains REVERT: B 225 TYR cc_start: 0.5500 (OUTLIER) cc_final: 0.5192 (m-10) REVERT: B 233 ASP cc_start: 0.8128 (t0) cc_final: 0.7662 (t0) REVERT: C 225 TYR cc_start: 0.5493 (OUTLIER) cc_final: 0.5185 (m-10) REVERT: C 233 ASP cc_start: 0.8124 (t0) cc_final: 0.7660 (t0) REVERT: F 225 TYR cc_start: 0.5495 (OUTLIER) cc_final: 0.5188 (m-10) REVERT: F 233 ASP cc_start: 0.8129 (t0) cc_final: 0.7660 (t0) REVERT: H 225 TYR cc_start: 0.5496 (OUTLIER) cc_final: 0.5186 (m-10) REVERT: H 233 ASP cc_start: 0.8129 (t0) cc_final: 0.7662 (t0) outliers start: 36 outliers final: 12 residues processed: 209 average time/residue: 1.1634 time to fit residues: 265.5143 Evaluate side-chains 169 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 225 TYR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 225 TYR Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 146 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12720 Z= 0.196 Angle : 0.534 9.089 17232 Z= 0.283 Chirality : 0.040 0.135 1928 Planarity : 0.005 0.053 2180 Dihedral : 4.017 15.891 1736 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.31 % Allowed : 19.73 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.22), residues: 1520 helix: 1.76 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.28 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 362 HIS 0.003 0.001 HIS B 306 PHE 0.023 0.001 PHE B 289 TYR 0.015 0.001 TYR B 188 ARG 0.011 0.000 ARG F 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 1.312 Fit side-chains REVERT: B 109 HIS cc_start: 0.7661 (p-80) cc_final: 0.5905 (m170) REVERT: B 233 ASP cc_start: 0.8045 (t0) cc_final: 0.7595 (t0) REVERT: B 346 GLU cc_start: 0.8863 (mm-30) cc_final: 0.7779 (tp30) REVERT: B 413 TYR cc_start: 0.5966 (OUTLIER) cc_final: 0.4583 (m-80) REVERT: B 415 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6724 (mt0) REVERT: C 233 ASP cc_start: 0.8042 (t0) cc_final: 0.7593 (t0) REVERT: C 346 GLU cc_start: 0.8861 (mm-30) cc_final: 0.7769 (tp30) REVERT: C 413 TYR cc_start: 0.5969 (OUTLIER) cc_final: 0.4587 (m-80) REVERT: C 415 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6732 (mt0) REVERT: F 233 ASP cc_start: 0.8045 (t0) cc_final: 0.7593 (t0) REVERT: F 346 GLU cc_start: 0.8857 (mm-30) cc_final: 0.7679 (tp30) REVERT: F 413 TYR cc_start: 0.5972 (OUTLIER) cc_final: 0.4584 (m-80) REVERT: F 415 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6732 (mt0) REVERT: H 233 ASP cc_start: 0.8047 (t0) cc_final: 0.7596 (t0) REVERT: H 310 LEU cc_start: 0.8603 (mp) cc_final: 0.8352 (mt) REVERT: H 346 GLU cc_start: 0.8855 (mm-30) cc_final: 0.7770 (tp30) REVERT: H 413 TYR cc_start: 0.5832 (OUTLIER) cc_final: 0.4357 (m-80) outliers start: 44 outliers final: 12 residues processed: 185 average time/residue: 1.1087 time to fit residues: 224.8019 Evaluate side-chains 172 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain C residue 415 GLN Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain F residue 415 GLN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN C 56 GLN F 56 GLN H 56 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12720 Z= 0.262 Angle : 0.574 9.121 17232 Z= 0.306 Chirality : 0.042 0.127 1928 Planarity : 0.005 0.054 2180 Dihedral : 4.123 17.249 1736 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.22 % Allowed : 18.98 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.21), residues: 1520 helix: 1.70 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.32 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 362 HIS 0.003 0.001 HIS B 306 PHE 0.021 0.002 PHE F 386 TYR 0.017 0.001 TYR B 188 ARG 0.008 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 170 time to evaluate : 1.408 Fit side-chains REVERT: B 109 HIS cc_start: 0.7665 (p-80) cc_final: 0.6042 (m170) REVERT: B 233 ASP cc_start: 0.8139 (t0) cc_final: 0.7678 (t0) REVERT: B 415 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6739 (mt0) REVERT: C 233 ASP cc_start: 0.8135 (t0) cc_final: 0.7675 (t0) REVERT: C 415 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6745 (mt0) REVERT: F 233 ASP cc_start: 0.8138 (t0) cc_final: 0.7676 (t0) REVERT: F 415 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6745 (mt0) REVERT: H 233 ASP cc_start: 0.8142 (t0) cc_final: 0.7679 (t0) outliers start: 56 outliers final: 24 residues processed: 206 average time/residue: 1.2292 time to fit residues: 277.0644 Evaluate side-chains 176 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain C residue 415 GLN Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 318 LYS Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain F residue 415 GLN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 318 LYS Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN C 56 GLN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 415 GLN H 416 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12720 Z= 0.218 Angle : 0.555 9.598 17232 Z= 0.289 Chirality : 0.041 0.145 1928 Planarity : 0.005 0.052 2180 Dihedral : 4.001 16.714 1736 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.64 % Allowed : 20.93 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.21), residues: 1520 helix: 1.76 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.28 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 362 HIS 0.003 0.001 HIS B 306 PHE 0.023 0.002 PHE F 289 TYR 0.016 0.001 TYR B 188 ARG 0.008 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 1.458 Fit side-chains REVERT: B 109 HIS cc_start: 0.7630 (p-80) cc_final: 0.6038 (m170) REVERT: B 169 GLN cc_start: 0.6970 (tm-30) cc_final: 0.6590 (tm-30) REVERT: B 233 ASP cc_start: 0.8055 (t0) cc_final: 0.7595 (t0) REVERT: B 346 GLU cc_start: 0.8875 (mm-30) cc_final: 0.7805 (tp30) REVERT: B 413 TYR cc_start: 0.5941 (OUTLIER) cc_final: 0.4553 (m-80) REVERT: C 169 GLN cc_start: 0.6974 (tm-30) cc_final: 0.6593 (tm-30) REVERT: C 233 ASP cc_start: 0.8052 (t0) cc_final: 0.7596 (t0) REVERT: C 346 GLU cc_start: 0.8874 (mm-30) cc_final: 0.7793 (tp30) REVERT: C 413 TYR cc_start: 0.5942 (OUTLIER) cc_final: 0.4560 (m-80) REVERT: F 169 GLN cc_start: 0.6979 (tm-30) cc_final: 0.6596 (tm-30) REVERT: F 233 ASP cc_start: 0.8056 (t0) cc_final: 0.7600 (t0) REVERT: F 346 GLU cc_start: 0.8868 (mm-30) cc_final: 0.7790 (tp30) REVERT: F 413 TYR cc_start: 0.5948 (OUTLIER) cc_final: 0.4552 (m-80) REVERT: H 169 GLN cc_start: 0.6973 (tm-30) cc_final: 0.6597 (tm-30) REVERT: H 233 ASP cc_start: 0.8062 (t0) cc_final: 0.7602 (t0) REVERT: H 346 GLU cc_start: 0.8867 (mm-30) cc_final: 0.7792 (tp30) REVERT: H 413 TYR cc_start: 0.5948 (OUTLIER) cc_final: 0.4314 (m-80) outliers start: 35 outliers final: 21 residues processed: 181 average time/residue: 1.1683 time to fit residues: 230.8028 Evaluate side-chains 179 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 73 optimal weight: 0.0970 chunk 95 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN C 56 GLN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12720 Z= 0.224 Angle : 0.556 9.231 17232 Z= 0.295 Chirality : 0.041 0.137 1928 Planarity : 0.005 0.052 2180 Dihedral : 3.997 16.817 1736 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.18 % Allowed : 21.23 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1520 helix: 1.76 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.25 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 362 HIS 0.003 0.001 HIS F 306 PHE 0.017 0.001 PHE C 386 TYR 0.016 0.001 TYR C 188 ARG 0.008 0.000 ARG H 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 1.427 Fit side-chains REVERT: B 109 HIS cc_start: 0.7646 (p-80) cc_final: 0.6034 (m170) REVERT: B 233 ASP cc_start: 0.8070 (t0) cc_final: 0.7608 (t0) REVERT: B 346 GLU cc_start: 0.8878 (mm-30) cc_final: 0.7820 (tp30) REVERT: B 413 TYR cc_start: 0.5952 (OUTLIER) cc_final: 0.4557 (m-80) REVERT: C 233 ASP cc_start: 0.8065 (t0) cc_final: 0.7606 (t0) REVERT: C 346 GLU cc_start: 0.8875 (mm-30) cc_final: 0.7809 (tp30) REVERT: C 413 TYR cc_start: 0.5951 (OUTLIER) cc_final: 0.4560 (m-80) REVERT: F 233 ASP cc_start: 0.8069 (t0) cc_final: 0.7607 (t0) REVERT: F 346 GLU cc_start: 0.8866 (mm-30) cc_final: 0.7797 (tp30) REVERT: F 413 TYR cc_start: 0.5952 (OUTLIER) cc_final: 0.4555 (m-80) REVERT: H 233 ASP cc_start: 0.8071 (t0) cc_final: 0.7611 (t0) REVERT: H 346 GLU cc_start: 0.8864 (mm-30) cc_final: 0.7797 (tp30) REVERT: H 413 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.4241 (m-80) outliers start: 29 outliers final: 21 residues processed: 178 average time/residue: 1.1678 time to fit residues: 227.2764 Evaluate side-chains 184 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 0.0050 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN C 56 GLN F 56 GLN H 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.221624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.186752 restraints weight = 13782.254| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 1.87 r_work: 0.3713 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12720 Z= 0.366 Angle : 0.628 8.687 17232 Z= 0.336 Chirality : 0.045 0.151 1928 Planarity : 0.006 0.053 2180 Dihedral : 4.351 20.670 1736 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.01 % Allowed : 20.48 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1520 helix: 1.50 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : -2.42 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 362 HIS 0.004 0.001 HIS H 306 PHE 0.031 0.002 PHE C 386 TYR 0.023 0.002 TYR H 188 ARG 0.008 0.001 ARG H 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4387.67 seconds wall clock time: 78 minutes 56.58 seconds (4736.58 seconds total)